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17 - Genome Mapping, Assembly, and Comparison

Published online by Cambridge University Press:  05 June 2012

Jin Xiong
Jin Xiong
Affiliation:
Texas A & M University
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Summary

Genomics is the study of genomes. Genomic studies are characterized by simultaneous analysis of a large number of genes using automated data gathering tools. The topics of genomics range from genome mapping, sequencing, and functional genomic analysis to comparative genomic analysis. The advent of genomics and the ensuing explosion of sequence information are the main driving force behind the rapid development of bioinformatics today.

Genomic study can be tentatively divided into structural genomics and functional genomics. Structural genomics refers to the initial phase of genome analysis, which includes construction of genetic and physical maps of a genome, identification of genes, annotation of gene features, and comparison of genome structures. This is the major theme of discussion of this chapter. However, it should to be mentioned that the term structural genomics has already been used by a structural biology group for an initiative to determine three-dimensional structures of all proteins in a cell. Strictly speaking, the initiative of structural determination of proteins falls within the realm of structural proteomics and should not be confused as a subdiscipline of genomics. The structure genomics discussed herein mainly deals with structures of genome sequences. Functional genomics refers to the analysis of global gene expression and gene functions in a genome, which is discussed in Chapter 18.

GENOME MAPPING

The first step to understanding a genome structure is through genome mapping, which is a process of identifying relative locations of genes, mutations or traits on a chromosome.

Type
Chapter
Information
Essential Bioinformatics , pp. 243 - 260
Publisher: Cambridge University Press
Print publication year: 2006

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References

Bennetzen, J. 2002. Opening the door to comparative plant biology. Science 296:60–3CrossRefGoogle ScholarPubMed
Chain, P., Kurtz, S., Ohlebusch, E., and Slezak, T. 2003. An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges. Brief. Bioinform. 4:105–23CrossRefGoogle ScholarPubMed
Dandekar, T, Snel, B., Huynen, M., and Bork, P. 1998. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci. 23:324–8CrossRefGoogle ScholarPubMed
Frazer, K. A., Elnitski, L., Church, D. M., Dubchak, I., and Hardison, R. C. 2003. Cross-species sequence comparisons: A review of methods and available resources. Genome Res. 13:1–12CrossRefGoogle ScholarPubMed
Gibson, G., and Muse, S. V. 2002. A Primer of Genome Science.Sunderland, MA: Sinauer AssociatesGoogle Scholar
Karlin, S., Mrazek, J., and Gentles, A. J. 2003. Genome comparisons and analysis. Curr. Opin. Struct. Biol. 13:344–52CrossRefGoogle ScholarPubMed
Lewis, R., and Palevitz, B. A. 2001. Genome economy. The Scientist 15:21Google Scholar
Lio, P. 2003. Statistical bioinformatic methods in microbial genome analysis. BioEssays 25:266–73CrossRefGoogle ScholarPubMed
Michalovich, D., Overington, J., and Fagan, R. 2002. Protein sequence analysis in silico: Application of structure-based bioinformatics to genomic initiatives. Curr. Opin. Pharmacol. 2:574–80CrossRefGoogle ScholarPubMed
Pennacchio, L. A., and Rubin, E. M. 2003. Comparative genomic tools and databases: Providing insights into the human genome. J. Clin. Invest. 111:1099–106CrossRefGoogle ScholarPubMed
Primrose, S. B., and Twyman, R. M. 2003. Principles of Genome Analysis and Genomics, 3rd ed. Oxford, UK: BlackwellGoogle Scholar
Stein, L. 2001. Genome annotation: From sequence to biology. Nat. Rev. Genetics 2:493–503CrossRefGoogle ScholarPubMed
Sterky, F., and Lundeberg, J. 2000. Sequence analysis of gene and genomes. J. Biotechnol. 76:1–31CrossRefGoogle ScholarPubMed
Ureta-Vidal, A., Ettwiller, L., and Birney, E. 2003. Comparative genomics: Genome-wide analysis of metazoan eukaryotes. Nature Rev. Genetics 4:251–62CrossRefGoogle ScholarPubMed
Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., Agarwala, R.. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–62Google ScholarPubMed
Wei, L., Liu, Y., Dubchak, I., Shon, J., and Park, J. 2002. Comparative genomics approaches to study organism similarities and differences. J. Biomed. Inform. 35:142–50CrossRefGoogle ScholarPubMed
Xiong, J., Fischer, W. M., Inoue, K., Nakahara, M., and Bauer, C. E. 2000. Molecular evidence for the early evolution of photosynthesis. Science 289:1724–30CrossRefGoogle ScholarPubMed

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